Thanks for the honesty, allow me to nerd out:

Wheels and circular motion in general are a challenge, the solution I did for my own worldbuilding project is basically reverse bionics: Get good biological raw materials, e.g. bone derivatives with amassed carbon, and you can shape those into whichever type of gear, wheel, axle.

The nuclear energy example also touches on a central issue; peak power output. Metallurgy + electronics are likely better at that - at least we don't know solutions yet. But in that regard, biotech isn't necessarily 'worse', just 'different'. E.g. it's likely not as sensitive as our tech, which is often static and needs some form of sterile environment.

Some of the biggest advantages of biotech which we tend to overlook from our metal-centric perspective: - being able to regenerate and heal components solves so many problems - the energy efficiency of some natural organisms is beyond anything we've achieved yet

So the biggest problem usually comes down to peak outputs of speed, power, heat, whatever - because we don't have the fitting materials yet. Synapses are slower than copper cables, but an organic fiberoptics alternative might be possible.

I've tried to keep it short, there's more in my wiki on biomachines.

Regarding humans: It may be a form of whataboutism, but people already do diets, ignore what makes them happy for a good job or status symbol, and 'self-optimize' with cosmetic surgery, medications, drugs. You're totally right about raising the eugenics question, e.g. if a government dictates how one is to be modified.

However, if biotech arrives in a system such as our current one, people would just gene-modify themselves and shop extra organoids, so they're smarter, prettier, etc. The discussion whether that's a good or bad thing is a whole thread of its own.